CCDC78

Last updated
CCDC78
Identifiers
Aliases CCDC78 , C16orf25, CNM4, JFP10, hsCcdc78, coiled-coil domain containing 78
External IDs OMIM: 614666 MGI: 2685784 HomoloGene: 105408 GeneCards: CCDC78
Orthologs
SpeciesHumanMouse
Entrez

124093

381077

Ensembl

ENSG00000162004

ENSMUSG00000071202

UniProt

A2IDD5

D3Z5T1

RefSeq (mRNA)

NM_001031737
NM_173476
NM_001378030
NM_001378031
NM_001378033

Contents

NM_001165929

RefSeq (protein)

NP_001026907
NP_001364959
NP_001364960
NP_001364962

NP_001159401

Location (UCSC) Chr 16: 0.72 – 0.73 Mb Chr 17: 26.01 – 26.01 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Coiled-coil domain-containing 78 (CCDC78) is a protein in humans encoded by the CCDC78 gene. It has several aliases including C16orf25, FLJ34512, CNM4, and JFP10. [5] It is located on the (-) strand on chromosome 16 (16p13.3). Its gene neighborhood includes NARFL (also on the minus strand), HAGHL, FAM173A, and METRN. The CCDC78 gene is 10,892 base pairs long, and the protein contains 438 amino acids. [6] The protein weighs approximately 4.852 KDal. [7] There are several isoforms, including one indicated with a unique congenital myopathy. [8] Several expression profiles show it has ubiquitous expression at moderate levels. Although no paralogs exist several orthologs do.

Function

The function of this gene is currently unknown. There is evidence that CCDC78 plays a role in skeletal muscle contraction. This is supported by structural similarities to other muscle proteins and by localization assays. CCDC78's predicted structure was similar to that of tropomyosin (see below). [9] The gene product is found primarily in the perinuclear region, the sarcolemmal membrane, and in the reticular pattern of the sarcoplasm. However, localization assays predict it to also be found in the cytoplasm. [8]

mRNA

Transcript Variants of CCDC78 according to AceView.png

General Properties: [6]

Transcript Variants: There are 13 known alternative splicing patterns. [5] These can be seen in the adjacent image. One of these is indicated in disease. [8]

Protein

General Properties: [7]

Expression

When looking at EST profiles in humans, CCDC78 seems to show ubiquitous expression at moderate levels. [6]

Predicted post-translational modification: Phosphorylation of several serine residues has been predicted by using tools at ExPasy. [10]

Predicted secondary structure

Secondary structure of CCDC78 was predicted using the protein secondary structure prediction tool PELE. As would be expected with a coiled-coil domain containing protein, there are several α-helices. [7] The model was predicted to be 98% accurate to 65% of the protein. The predicted image can be seen below. This predicted model is closely related to tropomyosin - a contractile protein. [9]

Protein-protein interactions

Only one protein has been found to interact with CCDC78. An analysis performed from IntAct showed an interaction between CCDC78 and dAK1_1 in Yersinia pestis. [11]

Homology

CCDC78 has no known paralogs in the human genome. However, it has several orthologs in other organisms. Orthologs can be found throughout the animal kingdom. CCDC78 is highly conserved in mammals. [7] The coiled-coil domain is highly conserved throughout all orthologs, demonstrating the importance of these domains.

Clinical relevance

A mutation in this gene has been shown to cause a unique congenital myopathy. [8] This mutation is caused by alternative splicing - a 222 bp in-frame insertion. A group of researchers from the University of Michigan analyzed a family with a dominantly inherited congenital myopathy. After linkage analysis followed by whole-exome capture and next-generation sequencing, they found CCDC78 to be present in affected individuals and absent in >10,000 controls. [8] They then successfully modeled this congenital myopathy in zebrafish. CCDC78 has also been associated with an immune response to Hepatitis B. [12]

Related Research Articles

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<span class="mw-page-title-main">CCDC144A</span> Protein-coding gene in humans

Coiled-coil domain-containing protein 144A is a protein that in humans is encoded by the CCDC144A gene. An alias of this gene is called KIAA0565. There are four members of the CCDC family: CCDC 144A, 144B, 144C and putative CCDC 144 N-terminal like proteins.

<span class="mw-page-title-main">FAM203B</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">CCDC94</span> Protein found in humans

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<span class="mw-page-title-main">Coiled-coil domain containing 42B</span> Protein found in humans

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<span class="mw-page-title-main">CCDC47</span> Protein-coding gene in humans

Coiled-coil domain 47 (CCDC47) is a gene located on human chromosome 17, specifically locus 17q23.3 which encodes for the protein CCDC47. The gene has several aliases including GK001 and MSTP041. The protein itself contains coiled-coil domains, the SEEEED superfamily, a domain of unknown function (DUF1682) and a transmembrane domain. The function of the protein is unknown, but it has been proposed that CCDC47 is involved in calcium ion homeostasis and the endoplasmic reticulum overload response.

<span class="mw-page-title-main">FAM71D</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">GPATCH11</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">VXN</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">Proser1</span>

PROSER1 is a protein that in humans is encoded by the PROSER1 gene.

<span class="mw-page-title-main">C14orf93</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">C12orf60</span> Protein-coding gene in humans

Uncharacterized protein C12orf60 is a protein that in humans is encoded by the C12orf60 gene. The gene is also known as LOC144608 or MGC47869. The protein lacks transmembrane domains and helices, but it is rich in alpha-helices. It is predicted to localize in the nucleus.

<span class="mw-page-title-main">PROB1</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">TMEM171</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">C22orf23</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">WD Repeat and Coiled Coil Containing Protein</span> Protein-coding gene in humans

WD Repeat and Coiled-coiled containing protein (WDCP) is a protein which in humans is encoded by the WDCP gene. The function of the protein is not completely understood, but WDCP has been identified in a fusion protein with anaplastic lymphoma kinase found in colorectal cancer. WDCP has also been identified in the MRN complex, which processes double-stranded breaks in DNA.

<span class="mw-page-title-main">MIPOL1</span> Protein-coding gene in the species Homo sapiens

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References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000162004 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000071202 - Ensembl, May 2017
  3. ↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. 1 2 GeneCards. "CCDC78 Gene". The Human Gene Compendium. Retrieved 2 May 2013.
  6. 1 2 3 "CCDC78". National Center for Biotechnology Information.
  7. 1 2 3 4 Biology WorkBench. San Diego Supercomputer Center http://seqtool.sdsc.edu/CGI/BW.cgi#!.{{cite web}}: Missing or empty |title= (help)[ permanent dead link ]
  8. 1 2 3 4 5 Majczenko K, Davidson AE, Camelo-Piragua S, Agrawal PB, Manfready RA, Li X, Joshi S, Xu J, Peng W, Beggs AH, Li JZ, Burmeister M, Dowling JJ (August 2012). "Dominant mutation of CCDC78 in a unique congenital myopathy with prominent internal nuclei and atypical cores". American Journal of Human Genetics. 91 (2): 365–71. doi:10.1016/j.ajhg.2012.06.012. PMC   3415545 . PMID   22818856.
  9. 1 2 "Phyre2". Structural Bioinformatics Group.[ permanent dead link ]
  10. ↑ "ExPASy: SIB Bioinformatics Resource Portal - Home". ExPasy. Swiss Institute of Bioinformatics.
  11. ↑ "3 binary interactions found for search term Ccdc78". IntAct Molecular Interaction Database. EMBL-EBI. Retrieved 2018-08-25.
  12. ↑ Davila S, Froeling FE, Tan A, Bonnard C, Boland GJ, Snippe H, Hibberd ML, Seielstad M (April 2010). "New genetic associations detected in a host response study to hepatitis B vaccine". Genes and Immunity. 11 (3): 232–8. doi:10.1038/gene.2010.1. PMID   20237496. S2CID   11183658.
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